Characterisation of the genetic diversity of indigenous sheep populations in Kenya using blood biochemical polymorphisms

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Abstract

Six indigenous sheep populations in Kenya generally classified as fat-tailed and
fat-rurnped hair types and one exotic breed (Merino) were analysed for variation at five
protein coding loci to determine the magnitude of genetic differentiation and
relationships among them. A total of 457 animals from farmers' flocks in Kwale,
Makueni, Siaya, Kakamega and Kajiado districts, for the fat-tailed and Isiolo district for
the fat-rurnped sheep were sampled. Forty animals of the fine wooled Merino breed were
used as the reference breed. Two genetically unrelated animals were bled per flock and
the blood typed for biochemical polymorphisms at the Albumin, Haemoglobin,
Transferrin, Esterase-A and Esterase-C loci, using polyacrylamide gels for Transferrin
and starch gel electrophoresis for Albumin, Haemoglobin, Esterase-A and Esterase-C.
The loci studied showed variability in the seven breeds with a total of 13 different alleles
being observed across the five loci. Albumin exhibited two alleles Albumin-S and
Albumin-F. Albumin-S was fixed in Kwale, Makueni, Siaya, Kakamega and Kajiado
populations. However both alleles were observed in the Isiolo and Merino populations
segregating at variable frequencies. Two alleles were also observed at the Haemoglobin
locus: Haemoglobin-A and Haemoglobin-B. Kwale, Makueni, Siaya and Isiolo were
monomorphic for Haemoglobin-B, but both alleles occurred at variable frequencies in
Kakamega, Kajiado and Merino populations. Transferrin was the most polymorphic
locus, with all the five most common alleles (TfA, TjB, TfC, TfD and TjE) observed in the
Merino, but only four (TfA, TjB, TfC and TfD) were observed in the indigenous sheep
populations in Kenya. TfE occurred exclusively in the Merino but not in any of the
indigenous sheep populations studied. Both Esterase-A and Esterase-C exhibited two
alleles each in all the breeds studied: the positive and negative variants. Abumin-S,
Haemoglobin-B, Transferrin-D, Esterase-A(-ve) and Esterase-C(-ve) predominated over
other alleles in all the populations studied. Within breed genetic diversity based on the
mean number of alleles per locus, percentage of polymorphic loci and average
heterozygosities was low in all the populations studied. The Kajiado population, which
showed the highest expected heterozygosity, and allelic diversity, was amongst the
populations that recorded the highest percentage of polymorphic loci. Kwale, Makueni
and Kakamega populations did not conform to the Hardy-Weinberg equilibrium with
respect to Transferrin locus. The FIs, FITand FSTmean values, as measures of population
differentiation across all loci were 0.318, 0.374 and 0.083 respectively. Pair-wise genetic
distances were estimated between population pairs using four genetic distance measures:
Nei's standard genetic distance (Ds), Nei's minimum genetic distance (Dm), Cavalli-
Sforza and Edwards chord (De) and arc (Da) distances. Within the indigenous sheep
populations in Kenya, the shortest distances were recorded between Kwale and Makueni
while the longest distances were observed between Kajiado and Siaya based on all the
four distance measures. However, the various indigenous sheep populations in Kenya
showed close genetic relationships. On average, Kajiado was the most genetically distant
population, recording the highest distances between itself and the rest of the indigenous
sheep populations studied. Generally, the overall distance between the Merino and the
indigenous sheep populations was as expected, high using all the distance matrices.
Phylogenies derived from pair-wise genetic distance estimates, show a clear separation
between the indigenous sheep populations studied and the exotic Merino. However, the
topology of the former showed rather poor consistency with their morphological
classification based on the localisation of fat deposits namely; fat-tailed and fat-rumped
hair sheep; suggesting either breed admixture or that the loci analysed do not have a lot to
do with the physical regions of fat deposits. The phylogenetic relationship between the
indigenous sheep populations revealed two distinct clusters. The first cluster grouped
together Kwale, Makueni, Siaya and Isiolo populations. Within this cluster, Kwale and
Makueni were grouped together and showed very close genetic relationship followed by
Siaya and Isiolo respectively. Kajiado and Kakamega populations were grouped
separately in the second cluster. Average genetic distances within and between the fattailed
and fat-rumped hair sheep as compared with previous studies of other indigenous
livestock breeds, showed that the genetic differentiation of each of the indigenous sheep
populations in Kenya is of the same order of magnitude as that among well-recognised
and established indigenous breeds of sheep from other countries.